Contacts of the helix formed by residues 139 - 168 (chain B) in PDB entry 2Y4T
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 139 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B SER* 3.0 9.6 + - - +
138B GLU* 1.3 77.2 - - - +
140B GLU* 1.3 61.9 + - + +
141B GLU 3.3 1.2 + - - -
142B LYS* 3.8 17.7 + - - +
143B GLU* 4.2 8.8 + - - +
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Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B THR* 3.5 18.5 + - - -
106B ALA* 3.5 31.3 + - - +
109B LEU* 3.8 23.4 - - + +
131B VAL* 4.8 4.2 - - + +
136B PRO* 3.7 8.6 - - + +
137B SER* 2.7 46.7 + - - +
139B ASN* 1.3 72.1 - - + +
141B GLU* 1.3 62.8 + - - +
142B LYS 3.3 0.2 - - - -
143B GLU* 3.5 3.6 + - - +
144B ALA* 3.0 24.8 + - - +
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Residues in contact with GLU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 4.2 17.4 - - + +
136B PRO* 3.7 31.3 - - + +
137B SER 3.3 7.2 + - - +
138B GLU* 3.7 24.8 - - - +
139B ASN 3.3 0.4 - - - -
140B GLU* 1.3 78.1 - - - +
142B LYS* 1.3 63.6 + - + +
144B ALA* 3.4 1.1 + - - +
145B GLN* 2.9 45.6 + - + +
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Residues in contact with LYS 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B GLU* 3.0 48.0 + - - +
139B ASN* 4.2 14.0 + - - +
140B GLU 3.3 0.6 - - - -
141B GLU* 1.3 85.5 + - + +
143B GLU* 1.3 63.1 + - + +
145B GLN* 4.2 4.6 - - - +
146B SER* 3.2 26.5 + - - -
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Residues in contact with GLU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU* 4.5 11.1 - - + +
113B HIS* 3.2 34.7 + - + +
139B ASN 4.2 5.7 + - - +
140B GLU* 3.5 8.7 + - - +
141B GLU 3.3 0.2 - - - -
142B LYS* 1.3 76.2 - - + +
144B ALA* 1.3 65.9 + - - +
145B GLN 3.2 0.2 + - - -
146B SER* 3.3 2.9 + - - -
147B GLN* 3.0 31.4 + - - +
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Residues in contact with ALA 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU* 3.7 23.8 - - + +
128B PHE* 3.6 27.7 - - + +
131B VAL* 3.9 12.3 - - + -
132B LEU* 3.8 19.5 - - + -
140B GLU 3.0 17.9 + - - +
141B GLU* 3.7 4.0 - - - +
143B GLU* 1.3 76.3 - - - +
145B GLN* 1.3 59.9 + - - +
148B LEU* 3.6 15.7 + - - +
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Residues in contact with GLN 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 3.8 26.5 - - + +
141B GLU* 2.9 29.1 + - - +
142B LYS* 4.2 4.5 - - - +
144B ALA* 1.3 74.0 - - - +
146B SER* 1.3 64.6 + - - +
147B GLN 3.2 1.6 - - - -
148B LEU* 3.0 21.2 + - + +
149B ILE* 3.2 17.4 + - + +
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Residues in contact with SER 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LYS 3.2 18.4 + - - -
143B GLU* 4.0 3.6 - - - -
145B GLN* 1.3 78.2 - - - +
147B GLN* 1.3 57.9 + - - +
149B ILE* 3.2 13.1 + - - +
150B LYS* 3.1 46.7 + - - +
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Residues in contact with GLN 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B HIS* 3.1 42.7 + - + +
116B LEU* 3.3 22.5 - - - +
128B PHE* 3.2 31.2 - - + -
143B GLU* 3.0 21.8 + - - +
144B ALA 4.0 1.1 - - - +
146B SER* 1.3 77.9 - - - +
148B LEU* 1.3 55.1 + - - +
150B LYS* 3.4 37.3 + - - +
151B SER* 2.8 29.1 + - - -
183B VAL* 5.5 0.6 - - - +
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLU* 3.9 34.5 - - + +
128B PHE* 3.5 28.3 - - + -
129B LYS* 4.3 19.7 - - + -
132B LEU* 4.0 23.3 - - + -
144B ALA 3.6 11.6 + - - +
145B GLN* 3.0 11.7 + - + +
147B GLN* 1.3 76.5 - - - +
149B ILE* 1.3 61.4 + - + +
151B SER* 3.7 2.2 - - - -
152B ASP* 2.8 44.9 + - - +
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Residues in contact with ILE 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B GLN* 3.6 14.6 - - + +
146B SER* 3.2 13.8 + - - +
148B LEU* 1.3 77.3 - - + +
150B LYS* 1.3 63.8 + - + +
152B ASP* 3.7 10.2 + - - +
153B GLU* 3.5 17.3 + - - +
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Residues in contact with LYS 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 4.6 1.1 - - + -
146B SER* 3.1 34.0 + - - +
147B GLN* 3.4 36.8 - - - +
149B ILE* 1.3 77.2 - - + +
151B SER* 1.3 57.7 + - - +
153B GLU* 3.1 9.3 + - - +
154B MET* 2.9 35.0 + - + +
183B VAL* 4.2 34.8 - - + -
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Residues in contact with SER 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 3.8 26.0 - - - +
121B LEU* 4.1 9.7 + - - +
125B GLU* 3.2 31.8 + - - +
128B PHE* 4.8 4.3 - - - -
147B GLN 2.8 21.1 + - - -
148B LEU* 3.3 8.3 + - - -
150B LYS* 1.3 73.8 - - - +
152B ASP* 1.3 58.3 + - - +
154B MET* 3.3 5.0 + - - +
155B GLN* 3.0 29.6 + - - +
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Residues in contact with ASP 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLU* 3.6 18.7 - - - +
148B LEU* 2.8 32.1 + - - +
149B ILE* 3.9 11.8 - - - +
151B SER* 1.3 71.6 - - - +
153B GLU* 1.3 61.8 + - - +
155B GLN* 3.4 16.4 - - - +
156B ARG* 3.4 8.0 + - - +
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Residues in contact with GLU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ILE 3.5 9.4 + - - +
150B LYS* 3.1 8.5 + - - +
152B ASP* 1.3 75.2 - - - +
154B MET* 1.3 77.0 + - - +
155B GLN 3.2 0.2 - - - -
156B ARG* 3.0 26.5 + - - +
157B LEU* 2.8 53.3 + - + +
179B LYS* 4.8 10.6 + - - +
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Residues in contact with MET 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 4.7 1.1 - - + -
121B LEU* 3.7 21.0 - - + +
150B LYS* 2.9 25.2 + - + +
151B SER* 3.5 10.8 - - - +
153B GLU* 1.3 100.7 - - - +
155B GLN* 1.3 53.7 + - - +
157B LEU* 3.2 15.9 + - + +
158B ARG* 2.8 36.2 + - - +
179B LYS 4.1 3.8 - - - +
180B ILE* 3.7 33.2 - - + +
183B VAL* 3.8 36.8 - - + -
184B CYS* 4.1 12.1 - - - -
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Residues in contact with GLN 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU* 3.4 31.5 - - - +
122B ASP* 2.9 24.2 + - - +
125B GLU* 2.8 29.3 - - - +
151B SER 3.0 8.9 + - - +
152B ASP* 3.4 13.7 - - - +
153B GLU 3.2 0.2 - - - -
154B MET* 1.3 77.1 - - - +
156B ARG* 1.3 59.7 + - - +
158B ARG* 3.9 7.2 - - - +
159B SER* 3.4 21.8 + - - -
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Residues in contact with ARG 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ASP 3.4 8.1 + - - +
153B GLU* 3.0 27.5 + - + +
155B GLN* 1.3 79.1 - - - +
157B LEU* 1.3 61.9 + - + +
159B SER* 3.5 6.8 + - - -
160B GLN* 3.1 46.2 + - + +
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Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B GLU* 2.8 36.8 + - + +
154B MET* 3.6 30.3 - - + +
156B ARG* 1.3 75.8 - - + +
158B ARG* 1.3 58.8 + - - +
160B GLN* 3.3 9.4 + - - +
161B ALA* 2.8 31.4 + - - +
176B PHE* 3.7 30.8 - - + +
179B LYS* 3.7 38.6 - - + -
180B ILE* 3.5 19.3 - - + +
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Residues in contact with ARG 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLY* 3.4 25.3 + - - -
121B LEU* 4.2 18.1 - - + +
154B MET 2.8 19.3 + - - +
155B GLN* 3.9 9.2 - - - +
156B ARG 3.4 0.2 - - - -
157B LEU* 1.3 72.5 - - - +
159B SER* 1.3 62.8 + - - +
161B ALA* 3.3 1.7 + - - +
162B LEU* 3.0 50.1 + - + +
180B ILE* 3.9 14.0 - - + +
187B ASP* 3.5 18.0 + - - -
189B GLU* 5.4 6.5 - - - +
190B LEU* 3.6 25.6 - - + +
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Residues in contact with SER 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B GLN 3.4 11.1 + - - -
156B ARG* 3.7 10.3 - - - -
157B LEU 3.4 0.4 - - - -
158B ARG* 1.3 78.9 - - - +
160B GLN* 1.3 58.0 + - - +
162B LEU* 4.1 7.3 - - - +
163B ASN* 3.0 30.5 + - - +
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Residues in contact with GLN 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ARG* 3.1 48.7 + - + +
157B LEU* 3.7 7.2 - - - +
158B ARG 3.2 0.2 - - - -
159B SER* 1.3 75.9 - - - +
161B ALA* 1.3 55.6 + - - +
163B ASN* 3.4 9.9 + - + +
164B ALA* 2.7 37.4 + - - +
176B PHE* 3.3 48.3 - - + -
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Residues in contact with ALA 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU 2.8 20.6 + - - +
158B ARG* 3.7 3.1 - - - +
160B GLN* 1.3 72.3 - - - +
162B LEU* 1.3 59.7 + - + +
164B ALA* 3.7 2.5 - - - +
165B PHE* 3.1 27.4 + - - +
173B ALA* 3.8 6.5 - - - +
176B PHE* 3.9 16.5 - - + +
177B LEU* 3.9 23.3 - - + -
180B ILE* 3.6 20.6 - - + -
190B LEU* 5.2 2.0 - - + -
193B LEU* 4.5 3.5 - - - +
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Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ARG* 3.0 48.8 + - + +
159B SER* 4.1 5.6 - - - +
161B ALA* 1.3 73.1 - - - +
163B ASN* 1.3 55.4 + - - +
165B PHE* 3.1 6.6 + - + +
166B GLY* 2.7 34.3 + - - -
190B LEU* 4.7 10.3 - - + -
193B LEU* 4.0 23.1 - - + -
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Residues in contact with ASN 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B SER* 3.0 21.2 + - - +
160B GLN* 3.4 12.1 + - - +
162B LEU* 1.3 74.9 - - - +
164B ALA* 1.3 64.8 + - - +
166B GLY* 3.3 2.6 + - - +
167B SER* 3.3 25.7 + - - -
176B PHE* 6.4 0.2 - - - -
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Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B GLN 2.7 21.1 + - - +
161B ALA 3.7 3.6 - - - +
163B ASN* 1.3 77.0 - - - +
165B PHE* 1.3 60.9 + - - +
167B SER* 3.2 10.9 + - - -
169B ASP* 2.9 44.6 + - + +
172B ALA* 4.1 10.3 - - + -
173B ALA* 3.7 17.5 - - - +
176B PHE* 4.2 7.4 - - + -
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Residues in contact with PHE 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ALA 3.1 18.5 + - - +
162B LEU* 3.5 4.5 - - - +
164B ALA* 1.3 75.8 - - - +
166B GLY* 1.3 68.6 + - - +
168B GLY* 3.1 14.6 + - - -
169B ASP 4.5 3.4 - - - +
170B TYR* 3.7 29.9 - + - -
173B ALA* 4.0 6.4 - - + +
193B LEU* 4.0 35.0 - - + -
196B GLU* 3.9 28.9 - - + -
197B CYS* 3.5 27.1 - - - -
200B LYS* 5.8 0.4 - - + -
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Residues in contact with GLY 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B LEU 2.7 19.0 + - - -
163B ASN* 3.3 3.3 + - - -
165B PHE* 1.3 80.6 - - - +
167B SER* 1.3 58.5 + - - +
168B GLY* 3.5 0.5 + - - -
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Residues in contact with SER 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ASN* 3.3 13.2 + - - -
164B ALA* 3.2 14.6 + - - -
165B PHE 3.3 0.2 - - - -
166B GLY* 1.3 75.9 - - - +
168B GLY* 1.3 56.6 + - - +
169B ASP* 3.6 10.0 + - - +
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Residues in contact with GLY 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ALA 3.9 0.2 - - - -
165B PHE 3.1 13.2 + - - -
166B GLY 3.3 1.0 - - - -
167B SER* 1.3 78.1 - - - +
169B ASP* 1.3 58.9 + - - +
170B TYR* 3.3 35.0 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il